Single-Cell Analysis of the Impact of Host Cell Heterogeneity on Infection with Foot-and-Mouth Disease Virus

Abstract

Viral infection and replication are affected by host cell heterogeneity, but the mechanisms underlying the effects remain unclear. Using single-cell analysis, we investigated the effects of host cell heterogeneity, including cell size, inclusion, and cell cycle, on foot-and-mouth disease virus (FMDV) infection (acute and persistent infections) and replication. We detected various viral genome replication levels in FMDV-infected cells. Large cells and cells with a high number of inclusions generated more viral RNA copies and viral protein and a higher proportion of infectious cells than other cells. Additionally, we found that the viral titer was 10- to 100-fold higher in cells in G/M than those in other cell cycle phases and identified a strong correlation between cell size, inclusion, and cell cycle heterogeneity, which all affected the infection and replication of FMDV. Furthermore, we demonstrated that host cell heterogeneity influenced the adsorption of FMDV due to differences in the levels of FMDV integrin receptors expression. Collectively, these results further our understanding of the evolution of a virus in a single host cell. It is important to understand how host cell heterogeneity affects viral infection and replication. Using single-cell analysis, we found that viral genome replication levels exhibited dramatic variability in foot-and-mouth disease virus (FMDV)-infected cells. We also found a strong correlation between heterogeneity in cell size, inclusion number, and cell cycle status and that all of these characteristics affect the infection and replication of FMDV. Moreover, we found that host cell heterogeneity influenced the viral adsorption as differences in the levels of FMDV integrin receptors' expression. This study provided new ideas for the studies of correlation between FMDV infection mechanisms and host cells.

Dissection of Influenza Infection In Vivo by Single-Cell RNA Sequencing

“…In that case, the infected and bystander cell populations should differ in their cell qualities. Such a difference is implausible, however, because the quality metrics of infected cells resemble those seen in bystanders ( Figures S3D and S3E), with the single notable exception of cell size, which, in agreement with earlier studies (Xin et al, 2018), is higher in the infected cells (Supplemental Information and Figures S3D-S3G).…”

“…For example, while epithelial cells are known to be the main targets of the influenza virus, several studies have documented that other cell types, such as endothelial cells, natural killer (NK) cells, macrophages, and dendritic cells (DCs), are also susceptible to the influenza virus, with potential implications of intracellular infection for their functionality (Manicassamy et al, 2010;McFadden et al, 2009). Complexity may also be related to a wide range of viral transcriptional states within the infected cells (Russell et al, 2018;Xin et al, 2018;Zanini et al, 2018), as well as to the heterogeneity of host-response states (Avraham et al, 2015). Another complication may be attributable to the dual role of the metabolic machinery in supporting the host while also limiting the energetic demands of the viral life cycle (Jovanovic et al, 2015;Kissig et al, 2017).…”

Cell-to-cell and genome-to-genome variability of Adenovirus transcription tuned by the cell cycle

“…In summary, our study demonstrates that the progression of AdV infection is variable at the single-cell and single genome levels, an observation that may apply to many other infections [10][11][12][13][14][15][16]. The strategy introduced in this study is highly versatile, and can be easily adapted to other viruses, non-viral transcripts or transgenes from viral vectors at the single-cell level in different cell types.…”

“…In principle, the cell autonomous aspects of the variable infection outcomes can be addressed by studying cell-to-cell variable parameters with purified virus inocula in defined cell types. For example, the cell-to-cell variable viral transcript counts and progeny yields have been observed with influenza, lymphocytic choriomeningitis, arenavirus, foot-and-mouth disease virus, Herpes simplex virus 1, murine gammaherpesvirus 68 and Dengue and Zika virus [10][11][12][13][14][15][16][17]. Studies with Influenza A virus revealed variability in translation and assembly of progeny particles [18,19].…”

Single-Cell Analysis Uncovers a Vast Diversity in Intracellular Viral Defective Interfering RNA Content Affecting the Large Cell-to-Cell Heterogeneity in Influenza A Virus Replication

“…Colors indicate the lower and upper 22.86% of cells with respect to the virus yield ("low" and "high", respectively), as shown in Figure 3B. Sample sizes from left to right (n = 5, 4, 35,27). *, p < 0.05; **, p < 0.005; n.s., p > 0.05, not significant (by the Wilcoxon rank sum test).…”